Plant small RNAs: advancement in the understanding of biogenesis and role in plant development

Singh, Archita; Gautam, Vibhav; Singh, Sharmila; Das, Shabari Sarkar; Verma, Swati; Mishra, Vishnu; Mukherjee, Shalini; Sarkar, Ananda K.

doi:10.1007/s00425-018-2927-5

Cited by 105 publications

(71 citation statements)

References 112 publications

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“…Having established and validated our experimental settings, a medium-scale screen was initiated with an in-house (Bayer) library of patented or previously described molecules known to influence plant growth and/or adaptation to stress, two processes notoriously regulated by endogenous PTGS pathways (Khraiwesh et al 2012;Deng et al 2018;Singh et al 2018). The identified SUL silencing modifiers were vastly dominated by enhancers representing ∼8% of molecules tested, which we studied in priority; in contrast, only 1.4% of the molecules were classified as inhibitors ( Fig.…”

Section: In Vitro Identification Of Robust Chemical Compounds That Enmentioning

confidence: 99%

Chemical enhancers of posttranscriptional gene silencing in Arabidopsis

Jay

Vitel²,

Brioudes

et al. 2019

RNA

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RNAi mediated by small-interfering RNAs (siRNAs) operates via transcriptional (TGS) and posttranscriptional gene silencing (PTGS). In Arabidopsis thaliana, TGS relies on DICER-LIKE-3 (DCL3)-dependent 24-nt siRNAs loaded into AGO4-clade ARGONAUTE effector proteins. PTGS operates via DCL4-dependent 21-nt siRNAs loaded into AGO1-clade proteins. We set up and validated a medium-throughput, semi-automatized procedure enabling chemical screening, in a 96-well in vitro format, of Arabidopsis transgenic seedlings expressing an inverted-repeat construct from the phloem companion cells. The ensuing quantitative PTGS phenotype was exploited to identify molecules, which, upon topical application, either inhibit or enhance siRNA biogenesis/activities. The vast majority of identified modifiers were enhancers, among which Sortin1, Isoxazolone, and [5-(3,4-dichlorophenyl)furan-2-yl]-piperidine-1-ylmethanethione (DFPM) provided the most robust and consistent results, including upon their application onto soil-grown plants in which their effect was nonautonomous and long lasting. The three molecules increased the RNAi potency of the inverted-repeat construct, in large part by enhancing 21-nt siRNA accumulation and loading into AGO1, and concomitantly reducing AGO4 and DCL3 levels in planta. A similar, albeit not identical effect, was observed on 22-nt siRNAs produced from a naturally occurring inverted-repeat locus, demonstrating that the molecules also enhance endogenous PTGS. In standardized assays conducted in seedling extracts, the three enhancers selectively increased DCL4-mediated processing of in vitro-synthesized double-stranded RNAs, indicating the targeting of a hitherto unknown PTGS component probably independent of the DCL4-cofactor DOUBLE-STRANDED RNA-BINDING 4 (DRB4). This study establishes the proof-of-concept that RNAi efficacy can be modulated by chemicals in a whole organism. Their potential applications and the associated future research are discussed.

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Section: In Vitro Identification Of Robust Chemical Compounds That Enmentioning

confidence: 99%

Chemical enhancers of posttranscriptional gene silencing in Arabidopsis

Jay

Vitel²,

Brioudes

et al. 2019

RNA

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“…In plant biology, the scientific literature regarding the role of miRNAs in plant development has increased significantly in recent years [20][21][22]. Many researchers have contributed some interesting and valuable review articles in this aspect focusing on the role of miRNAs in flower regulation and the development of single or multiple plant organs [23,24].…”

Section: Introductionmentioning

confidence: 99%

The Critical Role of miRNAs in Regulation of Flowering Time and Flower Development

Waheed

Zeng

2020

Genes

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Flowering is an important biological process for plants that ensures reproductive success. The onset of flowering needs to be coordinated with an appropriate time of year, which requires tight control of gene expression acting in concert to form a regulatory network. MicroRNAs (miRNAs) are non-coding RNAs known as master modulators of gene expression at the post-transcriptional level. Many different miRNA families are involved in flowering-related processes such as the induction of floral competence, floral patterning, and the development of floral organs. This review highlights the diverse roles of miRNAs in controlling the flowering process and flower development, in combination with potential biotechnological applications for miRNAs implicated in flower regulation.

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“…ta-siRNAs and miRNAs are the principal categories of plant sRNAs. They regulate plant development and growth by negatively controlling the expression of their target genes, mainly through transcriptional cleavage (Singh et al, 2018). Differently from animals, plant miRNAs targeting mechanism were initially believed to be the perfect or near-perfect match of the entire miRNA to the mRNA sequences.…”

Section: Introductionmentioning

confidence: 99%

Plant miRNAs Reduce Cancer Cell Proliferation by Targeting MALAT1 and NEAT1: A Beneficial Cross-Kingdom Interaction

Marzano

Caratozzolo

Consiglio³

et al. 2020

Front. Genet.

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MicroRNAs (miRNAs) are ubiquitous regulators of gene expression, evolutionarily conserved in plants and mammals. In recent years, although a growing number of papers debate the role of plant miRNAs on human gene expression, the molecular mechanisms through which this effect is achieved are still not completely elucidated. Some evidence suggest that this interaction might be sequence specific, and in this work, we investigated this possibility by transcriptomic and bioinformatics approaches. Plant and human miRNA sequences from primary databases were collected and compared for their similarities (global or local alignments). Out of 2,588 human miRNAs, 1,606 showed a perfect match of their seed sequence with the 5 end of 3,172 plant miRNAs. Further selections were applied based on the role of the human target genes or of the miRNA in cell cycle regulation (as an oncogene, tumor suppressor, or a biomarker for prognosis, or diagnosis in cancer). Based on these criteria, 20 human miRNAs were selected as potential functional analogous of 7 plant miRNAs, which were in turn transfected in different cell lines to evaluate their effect on cell proliferation. A significant decrease was observed in colorectal carcinoma HCT116 cell line. RNA-Seq demonstrated that 446 genes were differentially expressed 72 h after transfection. Noteworthy, we demonstrated that the plant mtr-miR-5754 and gma-miR4995 directly target the tumor-associated long non-coding RNA metastasisassociated lung adenocarcinoma transcript 1 (MALAT1) and nuclear paraspeckle assembly transcript 1 (NEAT1) in a sequence-specific manner. In conclusion, according to other recent discoveries, our study strengthens and expands the hypothesis that plant miRNAs can have a regulatory effect in mammals by targeting both protein-coding and non-coding RNA, thus suggesting new biotechnological applications.

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Plant small RNAs: advancement in the understanding of biogenesis and role in plant development

Cited by 105 publications

References 112 publications

Chemical enhancers of posttranscriptional gene silencing in Arabidopsis

Chemical enhancers of posttranscriptional gene silencing in Arabidopsis

The Critical Role of miRNAs in Regulation of Flowering Time and Flower Development

Plant miRNAs Reduce Cancer Cell Proliferation by Targeting MALAT1 and NEAT1: A Beneficial Cross-Kingdom Interaction

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